Add clustal output format as an option

[uzbit]

This is a preliminary pull request to add clustal output format. Now you can add the flag -output_format <fasta|clustal> and the appropriate output will be given, with default fasta as before.

This is work on closing issue #42 .

One thing that needs to be discussed, is that the output format for clustal is different between DNA/Amino, and so there should be some way of determining this from the input or as another flag maybe? Currently it just assumes AA, which will give misleading output for DNA.

[uzbit]

I decided to add a flag for sequence type, partially because I just want to move on, but also because ambiguous IUPAC codes can make the automatic determination of sequence type more difficult and not entirely reliable.

[agudys]

Hello @uzbit!
Thank you for your effort! I will take a look at your pull request ASAP.
Best,
Adam

[uzbit]

Ping!

[agudys]

@uzbit

Hello!
Sorry for not responding for such a long time. The latest revision of FAMSA we have been working recently includes serious refactorizations. This is why we restrained from merging your pull request. We are currently adding nucleotide mode to FAMSA and will include your pull request when adding this feature.

Best,
Adam